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apex-ruby 1.0.6

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data/ext/apex_ext/apex_src/documentation/docsets/Apex.docset/Contents/Resources/Documents/Citations.html ADDED Viewed

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+<!DOCTYPE html>
+<html lang="en">
+  <head>
+      <meta charset="UTF-8">
+      <meta name="viewport" content="width=device-width, initial-scale=1.0">
+      <meta name="generator" content="Apex 0.1.49">
+      <title>Document</title>
+      <style>
+        body {
+          font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Helvetica, Arial, sans-serif;
+          line-height: 1.6;
+          max-width: 800px;
+          margin: 2rem auto;
+          padding: 0 1rem;
+          color: #333;
+        }
+        pre { background: #f5f5f5; padding: 1rem; overflow-x: auto; }
+        code { background: #f0f0f0; padding: 0.2em 0.4em; border-radius: 3px; }
+        blockquote { border-left: 4px solid #ddd; margin: 0; padding-left: 1rem; color: #666; }
+        table { border-collapse: collapse; width: 100%%; }
+        th, td { border: 1px solid #ddd; padding: 0.5rem; }
+        th { background: #f5f5f5; }
+        tfoot td { background: #e8e8e8; }
+        figure.table-figure { width: fit-content; margin: 1em 0; }
+        figure.table-figure table { width: auto; }
+        figcaption { text-align: center; font-weight: bold; font-size: 0.8em; }
+        .page-break { page-break-after: always; }
+        .callout { padding: 1rem; margin: 1rem 0; border-left: 4px solid; }
+        .callout-note { border-color: #3b82f6; background: #eff6ff; }
+        .callout-warning { border-color: #f59e0b; background: #fffbeb; }
+        .callout-tip { border-color: #10b981; background: #f0fdf4; }
+        .callout-danger { border-color: #ef4444; background: #fef2f2; }
+        ins { background: #d4fcbc; text-decoration: none; }
+        del { background: #fbb6c2; text-decoration: line-through; }
+        mark { background: #fff3cd; }
+        .critic.comment { background: #e7e7e7; color: #666; font-style: italic; }
+      </style>
+  <style>
+/* Base styles */
+body {
+  -webkit-font-smoothing: antialiased;
+  -moz-osx-font-smoothing: grayscale;
+  font-size: 17px;
+  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
+    "Helvetica Neue", Arial, sans-serif;
+  line-height: 1.65;
+  color: #1e293b;
+  background-color: #fff;
+}
+/* Sidebar / Main TOC - wider on larger screens */
+.main-toc,
+.sidebar {
+  position: fixed;
+  left: 0;
+  top: 0;
+  width: auto;
+  min-width: 180px;
+  max-width: 250px;
+  height: 100vh;
+  overflow-y: auto;
+  background: #1e293b;
+  color: rgba(255, 255, 255, 0.9);
+  border-right: 2px solid rgba(255, 255, 255, 0.1);
+  padding: 24px 20px 130px;
+  font-size: 14px;
+  z-index: 100;
+  margin-right: 1rem;
+  box-shadow: 4px 0 24px rgba(0, 0, 0, 0.08);
+  transition: transform 0.3s ease;
+}
+.main-toc ul,
+.sidebar ul {
+  list-style: none;
+  padding-left: 0;
+  margin: 0;
+  padding-bottom: 80px;
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+  content: "";
+  display: block;
+  height: 80px;
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+  transition: all 0.15s ease;
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+  text-overflow: ellipsis;
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+  padding: 10px;
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+  font-size: 20px;
+  line-height: 1;
+  width: 44px;
+  height: 44px;
+  align-items: center;
+  justify-content: center;
+  box-shadow: 0 2px 8px rgba(0, 0, 0, 0.2);
+  transition: all 0.2s ease;
+  opacity: 0.2;
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+  background: #334155;
+  color: #fff;
+  opacity: 1;
+}
+/* Move hamburger to the right of the sidebar when menu is open */
+.hamburger-menu.active {
+  left: calc(
+    250px + 12px
+  ); /* Position just to the right of sidebar (max-width 250px + 12px padding) */
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+  background: #0ea5e9;
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+  content: "☰";
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+.hamburger-menu.active::before {
+  content: "✕";
+}
+/* Mobile menu overlay */
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+  display: none;
+  position: fixed;
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+  right: 0;
+  bottom: 0;
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+  z-index: 150;
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+  visibility: hidden;
+  transition: opacity 0.3s ease, visibility 0.3s ease;
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+  opacity: 1;
+  visibility: visible;
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+/* Page TOC */
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+  border: 1px solid #ddd;
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+  margin: 1.5rem 0;
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+  justify-content: flex-end;
+  padding-right: 2rem;
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+  visibility: visible;
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+  background: rgba(255, 255, 255, 0.95);
+  backdrop-filter: blur(10px);
+  border-bottom: 1px solid #ddd;
+  border-radius: 0 0 12px 12px;
+  box-shadow: 0 2px 8px rgba(0, 0, 0, 0.1);
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+  min-width: 200px;
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+  overflow: hidden;
+  transition: max-height 0.3s ease;
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+  max-height: 70vh;
+  overflow-y: auto;
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+  padding: 8px 16px 16px;
+  margin: 0;
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+  margin: 0.1em 0;
+}
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+  padding: 0.2em 0.5em;
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+  font-size: 13px;
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+  padding: 1rem;
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+  margin: 1em 0;
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+  padding: 0;
+  margin: 0;
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+/* Nested lists in page content */
+ul ul,
+ol ol,
+ul ol,
+ol ul {
+  padding-left: 1.5em;
+  margin-top: 0.25em;
+}
+/* Page footer */
+.page-footer {
+  background: #f5f5f5;
+  border-top: 1px solid #ddd;
+  padding: 1.5rem;
+  margin-top: 3rem;
+  color: #666;
+  font-size: 0.9em;
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+.page-footer p {
+  margin: 0.5em 0;
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+.page-footer a {
+  color: #0066cc;
+  text-decoration: none;
+}
+.page-footer a:hover {
+  text-decoration: underline;
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+/* Mobile responsive */
+@media (max-width: 768px) {
+  .hamburger-menu {
+    display: flex;
+  }
+  .main-toc,
+  .sidebar {
+    transform: translateX(-100%);
+    z-index: 175;
+  }
+  .main-toc.mobile-open,
+  .sidebar.mobile-open {
+    transform: translateX(0);
+  }
+  body {
+    margin-left: 0;
+  }
+  .floating-toc {
+    left: 0;
+  }
+}
+</style></head>
+  <body>
+<div class="floating-toc" id="floating-toc">
+  <div class="floating-toc-container">
+    <div class="floating-toc-header">
+      <span>Table of Contents 🔻</span>
+    </div>
+    <div class="floating-toc-content" id="floating-toc-content">
+      <!-- Content will be populated by JavaScript -->
+    </div>
+  </div>
+</div>
+<button class="hamburger-menu" id="hamburger-menu" aria-label="Toggle navigation"></button>
+<div class="mobile-menu-overlay" id="mobile-menu-overlay"></div>
+<nav class="main-toc"><ul><li><a href="Home.html">Home</a></li><li><a href="Getting-Started.html">Getting Started</a></li><li><a href="Installation.html">Installation</a></li><li><a href="Usage.html">Usage</a></li><li><a href="Syntax.html">Syntax</a></li><li><a href="Inline-Attribute-Lists.html">Inline Attribute Lists</a></li><li><a href="Modes.html">Modes</a></li><li><a href="Command-Line-Options.html">Command Line Options</a></li><li><a href="Multi-File-Documents.html">Multi-file Documents</a></li><li><a href="Citations.html">Citations</a></li><li><a href="Metadata-Transforms.html">Metadata Transforms</a></li><li><a href="Pandoc-Integration.html">Integrating with Pandoc</a></li><li><a href="Header-IDs.html">Header IDs</a></li><li><a href="C-API.html">C API</a></li><li><a href="Xcode-Integration.html">Xcode Integration</a></li><li><a href="Examples.html">Examples</a></li><li><a href="Plugins.html">Plugins</a></li><li><a href="Troubleshooting.html">Troubleshooting</a></li><li><a href="Credits.html">Credits</a></li></ul></nav>
+    <h1 id="citations-and-bibliography">
+      Citations and Bibliography
+    </h1>
+<nav class="page-toc" id="page-toc-top"><ul><li><a href="#citations-and-bibliography">Citations and Bibliography</a><ul><li><a href="#quick-start">Quick Start</a></li><li><a href="#citation-syntaxes">Citation Syntaxes</a><ul><li><a href="#pandoc-syntax">Pandoc Syntax</a></li><li><a href="#multimarkdown-syntax">MultiMarkdown Syntax</a></li><li><a href="#mmark-syntax">mmark Syntax</a></li></ul></li><li><a href="#bibliography-formats">Bibliography Formats</a><ul><li><a href="#bibtex-bib">BibTeX (.bib)</a></li><li><a href="#csl-json-json">CSL JSON (.json)</a></li><li><a href="#csl-yaml-yml-yaml">CSL YAML (.yml, .yaml)</a></li></ul></li><li><a href="#specifying-bibliography">Specifying Bibliography</a><ul><li><a href="#command-line">Command Line</a></li><li><a href="#document-metadata">Document Metadata</a></li></ul></li><li><a href="#bibliography-generation">Bibliography Generation</a></li><li><a href="#citation-options">Citation Options</a><ul><li><a href="#link-citations">Link Citations</a></li><li><a href="#suppress-bibliography">Suppress Bibliography</a></li><li><a href="#citation-style-csl">Citation Style (CSL)</a></li></ul></li><li><a href="#mode-support">Mode Support</a></li><li><a href="#performance">Performance</a></li><li><a href="#related">Related</a></li></ul></li></ul></nav>
+    <p>
+      Apex supports citations and bibliographies with multiple syntax styles and bibliography formats. Citations are processed in <strong>MultiMarkdown</strong> and <strong>unified</strong> modes.
+    </p>
+    <h2 id="quick-start">
+      Quick Start
+    </h2>
+    <p>
+<strong>      1. Create a bibliography file:</strong>
+    </p>
+    <p>
+      Create a BibTeX file (<code>references.bib</code>):
+    </p>
+<pre><code class="highlight language-bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">doe99</span><span class="p">,</span>
+  <span class="na">author</span> <span class="p">=</span> <span class="s">{Doe, John}</span><span class="p">,</span>
+  <span class="na">title</span> <span class="p">=</span> <span class="s">{Article Title}</span><span class="p">,</span>
+  <span class="na">journal</span> <span class="p">=</span> <span class="s">{Journal Name}</span><span class="p">,</span>
+  <span class="na">year</span> <span class="p">=</span> <span class="s">{1999}</span><span class="p">,</span>
+  <span class="na">volume</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span>
+  <span class="na">pages</span> <span class="p">=</span> <span class="s">{1--10}</span>
+<span class="p">}</span>
+<span class="nc">@book</span><span class="p">{</span><span class="nl">smith2000</span><span class="p">,</span>
+  <span class="na">author</span> <span class="p">=</span> <span class="s">{Smith, Jane}</span><span class="p">,</span>
+  <span class="na">title</span> <span class="p">=</span> <span class="s">{Book Title}</span><span class="p">,</span>
+  <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Publisher}</span><span class="p">,</span>
+  <span class="na">year</span> <span class="p">=</span> <span class="s">{2000}</span>
+<span class="p">}</span>
+</code></pre>
+  <p>
+<strong>    2. Add citations to your document:</strong>
+  </p>
+<pre><code class="highlight language-markdown"><span class="nn">---</span>
+<span class="na">bibliography</span><span class="pi">:</span> <span class="s">references.bib</span>
+<span class="nn">---</span>
+See [@doe99] for details. Smith discusses this in [@smith2000].
+<span class="gu">## References</span>
+<span class="c">&lt;!-- REFERENCES --&gt;</span>
+</code></pre>
+<p>
+<strong>  3. Process with Apex:</strong>
+</p>
+<pre><code class="highlight language-bash">apex document.md <span class="nt">--bibliography</span> references.bib
+</code></pre>
+<p>
+  Or specify in metadata (as shown above) and just run:
+</p>
+<pre><code class="highlight language-bash">apex document.md
+</code></pre>
+<h2 id="citation-syntaxes">
+  Citation Syntaxes
+</h2>
+<p>
+  Apex supports three citation syntax styles, automatically detected in unified mode:
+</p>
+<h3 id="pandoc-syntax">
+  Pandoc Syntax
+</h3>
+<p>
+  Pandoc-style citations use square brackets with <code>@</code> prefix:
+</p>
+<p>
+<strong>  Basic citation:</strong>
+</p>
+<pre><code class="highlight language-markdown">See [@doe99] for details.
+</code></pre>
+<p>
+<strong>  Multiple citations:</strong>
+</p>
+<pre><code class="highlight language-markdown">See [@doe99; @smith2000; @smith2004] for more information.
+</code></pre>
+<p>
+<strong>  Author in text:</strong>
+</p>
+<pre><code class="highlight language-markdown">@smith04 says blah.
+</code></pre>
+<p>
+<strong>  Author suppressed (year only):</strong>
+</p>
+<pre><code class="highlight language-markdown">Smith says blah [-@smith04].
+</code></pre>
+<p>
+<strong>  With locator (page numbers):</strong>
+</p>
+<pre><code class="highlight language-markdown">@smith04 [p. 33] says blah.
+See @doe99, pp. 33-35 and <span class="ge">*passim*</span>.
+</code></pre>
+<p>
+<strong>  Output:</strong>
+</p>
+<pre><code class="highlight language-html"><span class="nt">&lt;p&gt;</span>See <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"doe99"</span><span class="nt">&gt;</span>(Doe, John 1999)<span class="nt">&lt;/span&gt;</span> for details.<span class="nt">&lt;/p&gt;</span>
+<span class="nt">&lt;p&gt;</span>See <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"doe99 smith2000 smith2004"</span><span class="nt">&gt;</span>(Doe, John 1999; Smith, Jane 2000, 2004)<span class="nt">&lt;/span&gt;</span> for more information.<span class="nt">&lt;/p&gt;</span>
+<span class="nt">&lt;p&gt;&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"smith04"</span><span class="nt">&gt;</span>Smith, John (2004)<span class="nt">&lt;/span&gt;</span> says blah.<span class="nt">&lt;/p&gt;</span>
+<span class="nt">&lt;p&gt;</span>Smith says blah <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"smith04"</span><span class="nt">&gt;</span>(2004)<span class="nt">&lt;/span&gt;</span>.<span class="nt">&lt;/p&gt;</span>
+</code></pre>
+<h3 id="multimarkdown-syntax">
+  MultiMarkdown Syntax
+</h3>
+<p>
+  MultiMarkdown-style citations use <code>#</code> prefix:
+</p>
+<p>
+<strong>  Basic citation:</strong>
+</p>
+<pre><code class="highlight language-markdown">This is a statement[#Doe:2006].
+</code></pre>
+<p>
+<strong>  With locator:</strong>
+</p>
+<pre><code class="highlight language-markdown">This is a statement<span class="p">[</span><span class="nv">p. 23</span><span class="p">][</span><span class="ss">#Doe:2006</span><span class="p">]</span>.
+</code></pre>
+<p>
+<strong>  Empty locator:</strong>
+</p>
+<pre><code class="highlight language-markdown">This is a statement<span class="p">[][</span><span class="ss">#Doe:2006</span><span class="p">]</span>.
+</code></pre>
+<p>
+<strong>  Inline citation:</strong>
+</p>
+<pre><code class="highlight language-markdown">As per Doe.[#John Doe. <span class="ge">*A Totally Fake Book 1*</span>. Vanity Press, 2006.]
+</code></pre>
+<p>
+<strong>  Output:</strong>
+</p>
+<pre><code class="highlight language-html"><span class="nt">&lt;p&gt;</span>This is a statement<span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"Doe:2006"</span><span class="nt">&gt;</span>(Doe:2006)<span class="nt">&lt;/span&gt;</span>.<span class="nt">&lt;/p&gt;</span>
+<span class="nt">&lt;p&gt;</span>This is a statement[p. 23]<span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"Doe:2006"</span><span class="nt">&gt;</span>(Doe:2006)<span class="nt">&lt;/span&gt;</span>.<span class="nt">&lt;/p&gt;</span>
+</code></pre>
+<h3 id="mmark-syntax">
+  mmark Syntax
+</h3>
+<p>
+  mmark-style citations use <code>@</code> prefix (similar to Pandoc but with different conventions):
+</p>
+<p>
+<strong>  Basic citation:</strong>
+</p>
+<pre><code class="highlight language-markdown">This references [@RFC2535].
+</code></pre>
+<p>
+<strong>  Normative citation:</strong>
+</p>
+<pre><code class="highlight language-markdown">This references [@!RFC1034] (normative).
+</code></pre>
+<p>
+<strong>  Multiple citations:</strong>
+</p>
+<pre><code class="highlight language-markdown">Multiple citations: [@RFC1034;@RFC1035].
+</code></pre>
+<p>
+<strong>  Combined reference:</strong>
+</p>
+<pre><code class="highlight language-markdown">Combined reference: [@RFC1034@STD3].
+</code></pre>
+<p>
+<strong>  Output:</strong>
+</p>
+<pre><code class="highlight language-html"><span class="nt">&lt;p&gt;</span>This references <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"RFC2535"</span><span class="nt">&gt;</span>(RFC2535)<span class="nt">&lt;/span&gt;</span>.<span class="nt">&lt;/p&gt;</span>
+<span class="nt">&lt;p&gt;</span>Multiple citations: <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"RFC1034"</span><span class="nt">&gt;</span>(RFC1034)<span class="nt">&lt;/span&gt;</span>;<span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"RFC1035"</span><span class="nt">&gt;</span>(RFC1035)<span class="nt">&lt;/span&gt;</span>.<span class="nt">&lt;/p&gt;</span>
+</code></pre>
+<h2 id="bibliography-formats">
+  Bibliography Formats
+</h2>
+<p>
+  Apex supports three bibliography formats:
+</p>
+<h3 id="bibtex-bib">
+  BibTeX (<code>.bib</code>)
+</h3>
+<p>
+  Standard BibTeX format:
+</p>
+<pre><code class="highlight language-bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">doe99</span><span class="p">,</span>
+  <span class="na">author</span> <span class="p">=</span> <span class="s">{Doe, John}</span><span class="p">,</span>
+  <span class="na">title</span> <span class="p">=</span> <span class="s">{Article Title}</span><span class="p">,</span>
+  <span class="na">journal</span> <span class="p">=</span> <span class="s">{Journal Name}</span><span class="p">,</span>
+  <span class="na">year</span> <span class="p">=</span> <span class="s">{1999}</span><span class="p">,</span>
+  <span class="na">volume</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span>
+  <span class="na">pages</span> <span class="p">=</span> <span class="s">{1--10}</span>
+<span class="p">}</span>
+<span class="nc">@book</span><span class="p">{</span><span class="nl">smith2000</span><span class="p">,</span>
+  <span class="na">author</span> <span class="p">=</span> <span class="s">{Smith, Jane}</span><span class="p">,</span>
+  <span class="na">title</span> <span class="p">=</span> <span class="s">{Book Title}</span><span class="p">,</span>
+  <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Publisher}</span><span class="p">,</span>
+  <span class="na">year</span> <span class="p">=</span> <span class="s">{2000}</span>
+<span class="p">}</span>
+</code></pre>
+<h3 id="csl-json-json">
+  CSL JSON (<code>.json</code>)
+</h3>
+<p>
+  Citation Style Language JSON format:
+</p>
+<pre><code class="highlight language-json"><span class="p">[</span><span class="w">
+  </span><span class="p">{</span><span class="w">
+    </span><span class="nl">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"doe99"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"type"</span><span class="p">:</span><span class="w"> </span><span class="s2">"article-journal"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"title"</span><span class="p">:</span><span class="w"> </span><span class="s2">"Article Title"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"author"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="w">
+      </span><span class="p">{</span><span class="w">
+        </span><span class="nl">"family"</span><span class="p">:</span><span class="w"> </span><span class="s2">"Doe"</span><span class="p">,</span><span class="w">
+        </span><span class="nl">"given"</span><span class="p">:</span><span class="w"> </span><span class="s2">"John"</span><span class="w">
+      </span><span class="p">}</span><span class="w">
+    </span><span class="p">],</span><span class="w">
+    </span><span class="nl">"container-title"</span><span class="p">:</span><span class="w"> </span><span class="s2">"Journal Name"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"issued"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="w">
+      </span><span class="nl">"date-parts"</span><span class="p">:</span><span class="w"> </span><span class="p">[[</span><span class="mi">1999</span><span class="p">]]</span><span class="w">
+    </span><span class="p">},</span><span class="w">
+    </span><span class="nl">"volume"</span><span class="p">:</span><span class="w"> </span><span class="s2">"1"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"page"</span><span class="p">:</span><span class="w"> </span><span class="s2">"1-10"</span><span class="w">
+  </span><span class="p">}</span><span class="w">
+</span><span class="p">]</span><span class="w">
+</span></code></pre>
+<h3 id="csl-yaml-yml-yaml">
+  CSL YAML (<code>.yml</code>, <code>.yaml</code>)
+</h3>
+<p>
+  Citation Style Language YAML format:
+</p>
+<pre><code class="highlight language-yaml"><span class="pi">-</span> <span class="na">id</span><span class="pi">:</span> <span class="s">doe99</span>
+  <span class="na">type</span><span class="pi">:</span> <span class="s">article-journal</span>
+  <span class="na">title</span><span class="pi">:</span> <span class="s">Article Title</span>
+  <span class="na">author</span><span class="pi">:</span>
+    <span class="pi">-</span> <span class="na">family</span><span class="pi">:</span> <span class="s">Doe</span>
+      <span class="na">given</span><span class="pi">:</span> <span class="s">John</span>
+  <span class="na">container-title</span><span class="pi">:</span> <span class="s">Journal Name</span>
+  <span class="na">issued</span><span class="pi">:</span>
+    <span class="na">date-parts</span><span class="pi">:</span>
+      <span class="pi">-</span> <span class="pi">-</span> <span class="m">1999</span>
+  <span class="na">volume</span><span class="pi">:</span> <span class="m">1</span>
+  <span class="na">page</span><span class="pi">:</span> <span class="s">1-10</span>
+</code></pre>
+<h2 id="specifying-bibliography">
+  Specifying Bibliography
+</h2>
+<h3 id="command-line">
+  Command Line
+</h3>
+<pre><code class="highlight language-bash"><span class="c"># Single file</span>
+apex document.md <span class="nt">--bibliography</span> references.bib
+<span class="c"># Multiple files</span>
+apex document.md <span class="nt">--bibliography</span> refs1.bib <span class="nt">--bibliography</span> refs2.bib
+<span class="c"># With base directory</span>
+apex document.md <span class="nt">--bibliography</span> refs.bib <span class="nt">--base-dir</span> /path/to/docs
+</code></pre>
+<h3 id="document-metadata">
+  Document Metadata
+</h3>
+<p>
+<strong>  YAML front matter:</strong>
+</p>
+<pre><code class="highlight language-markdown"><span class="nn">---</span>
+<span class="na">bibliography</span><span class="pi">:</span> <span class="s">references.bib</span>
+<span class="nn">---</span>
+See [@doe99] for details.
+</code></pre>
+<p>
+<strong>  Multiple files:</strong>
+</p>
+<pre><code class="highlight language-markdown"><span class="nn">---</span>
+<span class="na">bibliography</span><span class="pi">:</span>
+  <span class="pi">-</span> <span class="s">refs1.bib</span>
+  <span class="pi">-</span> <span class="s">refs2.bib</span>
+<span class="nn">---</span>
+See [@doe99] for details.
+</code></pre>
+<p>
+<strong>  MultiMarkdown metadata:</strong>
+</p>
+<pre><code class="highlight language-markdown">Bibliography: references.bib
+See [@doe99] for details.
+</code></pre>
+<p>
+<strong>  Pandoc title block:</strong>
+</p>
+<pre><code class="highlight language-markdown">% Bibliography: references.bib
+See [@doe99] for details.
+</code></pre>
+<h2 id="bibliography-generation">
+  Bibliography Generation
+</h2>
+<p>
+  Bibliography is automatically generated from all cited entries and inserted at the <code>&lt;!-- REFERENCES --&gt;</code> marker:
+</p>
+<pre><code class="highlight language-markdown">See [@doe99] and [@smith2000] for details.
+<span class="gu">## References</span>
+<span class="c">&lt;!-- REFERENCES --&gt;</span>
+</code></pre>
+<p>
+<strong>  Output:</strong>
+</p>
+<pre><code class="highlight language-html"><span class="nt">&lt;p&gt;</span>See <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"doe99"</span><span class="nt">&gt;</span>(Doe, John 1999)<span class="nt">&lt;/span&gt;</span> and <span class="nt">&lt;span</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"smith2000"</span><span class="nt">&gt;</span>(Smith, Jane 2000)<span class="nt">&lt;/span&gt;</span> for details.<span class="nt">&lt;/p&gt;</span>
+<span class="nt">&lt;h2&gt;</span>References<span class="nt">&lt;/h2&gt;</span>
+<span class="nt">&lt;div</span> <span class="na">id=</span><span class="s">"refs"</span> <span class="na">class=</span><span class="s">"references csl-bib-body"</span><span class="nt">&gt;</span>
+<span class="nt">&lt;div</span> <span class="na">id=</span><span class="s">"ref-doe99"</span> <span class="na">class=</span><span class="s">"csl-entry"</span><span class="nt">&gt;</span>Doe, John 1999. <span class="nt">&lt;em&gt;</span>Article Title<span class="nt">&lt;/em&gt;</span>. <span class="nt">&lt;em&gt;</span>Journal Name<span class="nt">&lt;/em&gt;</span> 1: 1--10<span class="nt">&lt;/div&gt;</span>
+<span class="nt">&lt;div</span> <span class="na">id=</span><span class="s">"ref-smith2000"</span> <span class="na">class=</span><span class="s">"csl-entry"</span><span class="nt">&gt;</span>Smith, Jane 2000. <span class="nt">&lt;em&gt;</span>Book Title<span class="nt">&lt;/em&gt;</span>. Publisher<span class="nt">&lt;/div&gt;</span>
+<span class="nt">&lt;/div&gt;</span>
+</code></pre>
+<p>
+  If no <code>&lt;!-- REFERENCES --&gt;</code> marker is found, the bibliography is appended to the end of the document.
+</p>
+<h2 id="citation-options">
+  Citation Options
+</h2>
+<h3 id="link-citations">
+  Link Citations
+</h3>
+<p>
+  Use <code>--link-citations</code> to make citations link to their bibliography entries:
+</p>
+<pre><code class="highlight language-bash">apex document.md <span class="nt">--bibliography</span> refs.bib <span class="nt">--link-citations</span>
+</code></pre>
+<p>
+<strong>  Output:</strong>
+</p>
+<pre><code class="highlight language-html"><span class="nt">&lt;p&gt;</span>See <span class="nt">&lt;a</span> <span class="na">href=</span><span class="s">"#ref-doe99"</span> <span class="na">class=</span><span class="s">"citation"</span> <span class="na">data-cites=</span><span class="s">"doe99"</span><span class="nt">&gt;</span>(Doe, John 1999)<span class="nt">&lt;/a&gt;</span> for details.<span class="nt">&lt;/p&gt;</span>
+</code></pre>
+<h3 id="suppress-bibliography">
+  Suppress Bibliography
+</h3>
+<p>
+  Use <code>--no-bibliography</code> to suppress bibliography output while still processing citations:
+</p>
+<pre><code class="highlight language-bash">apex document.md <span class="nt">--bibliography</span> refs.bib <span class="nt">--no-bibliography</span>
+</code></pre>
+<h3 id="citation-style-csl">
+  Citation Style (CSL)
+</h3>
+<p>
+  Specify a Citation Style Language file to control citation and bibliography formatting:
+</p>
+<pre><code class="highlight language-bash">apex document.md <span class="nt">--bibliography</span> refs.bib <span class="nt">--csl</span> apa.csl
+</code></pre>
+<p>
+  CSL files can also be specified in metadata:
+</p>
+<pre><code class="highlight language-markdown"><span class="nn">---</span>
+<span class="na">bibliography</span><span class="pi">:</span> <span class="s">refs.bib</span>
+<span class="na">csl</span><span class="pi">:</span> <span class="s">apa.csl</span>
+<span class="nn">---</span>
+</code></pre>
+<h2 id="mode-support">
+  Mode Support
+</h2>
+<p>
+<strong>  Unified mode:</strong>
+</p>
+<ul>
+  <li>
+    All citation syntaxes supported (auto-detected)
+  </li>
+  <li>
+    All bibliography formats supported
+  </li>
+  <li>
+    Citations enabled by default when bibliography is provided
+  </li>
+</ul>
+<p>
+<strong>  MultiMarkdown mode:</strong>
+</p>
+<ul>
+  <li>
+    MultiMarkdown citation syntax (<code>[#key]</code>)
+  </li>
+  <li>
+    All bibliography formats supported
+  </li>
+  <li>
+    Citations enabled by default when bibliography is provided
+  </li>
+</ul>
+<p>
+<strong>  CommonMark/GFM modes:</strong>
+</p>
+<ul>
+  <li>
+    Citations disabled (pure CommonMark/GFM)
+  </li>
+</ul>
+<p>
+<strong>  Kramdown mode:</strong>
+</p>
+<ul>
+  <li>
+    Citations disabled (Kramdown uses different citation system)
+  </li>
+</ul>
+<h2 id="performance">
+  Performance
+</h2>
+<p>
+  Citations are only processed when a bibliography is actually provided (via <code>--bibliography</code> flag or metadata). This ensures no performance impact when citations aren’t being used.
+</p>
+<h2 id="related">
+  Related
+</h2>
+<ul>
+  <li>
+<a href="Command-Line-Options.html">    Command Line Options</a> - Citation-related CLI flags
+  </li>
+  <li>
+<a href="Syntax.html">    Syntax</a> - Citation syntax reference
+  </li>
+  <li>
+<a href="Modes.html">    Modes</a> - Mode-specific citation support
+  </li>
+</ul>
+<script>
+// Hamburger menu functionality
+(function() {
+  function initHamburgerMenu() {
+    var hamburger = document.getElementById('hamburger-menu');
+    var sidebar = document.querySelector('.main-toc, .sidebar');
+    var overlay = document.getElementById('mobile-menu-overlay');
+    if (!hamburger || !sidebar) return;
+    function toggleMenu() {
+      var isOpen = sidebar.classList.contains('mobile-open');
+      if (isOpen) {
+        sidebar.classList.remove('mobile-open');
+        hamburger.classList.remove('active');
+        if (overlay) overlay.classList.remove('active');
+      } else {
+        sidebar.classList.add('mobile-open');
+        hamburger.classList.add('active');
+        if (overlay) overlay.classList.add('active');
+      }
+    }
+    hamburger.addEventListener('click', function(e) {
+      e.stopPropagation();
+      toggleMenu();
+    });
+    if (overlay) {
+      overlay.addEventListener('click', function() {
+        toggleMenu();
+      });
+    }
+    // Close menu when clicking on a sidebar link (mobile only)
+    if (window.innerWidth <= 768) {
+      var sidebarLinks = sidebar.querySelectorAll('a');
+      sidebarLinks.forEach(function(link) {
+        link.addEventListener('click', function() {
+          setTimeout(function() {
+            sidebar.classList.remove('mobile-open');
+            hamburger.classList.remove('active');
+            if (overlay) overlay.classList.remove('active');
+          }, 100);
+        });
+      });
+    }
+    // Close menu on window resize if going to desktop
+    window.addEventListener('resize', function() {
+      if (window.innerWidth > 768) {
+        sidebar.classList.remove('mobile-open');
+        hamburger.classList.remove('active');
+        if (overlay) overlay.classList.remove('active');
+      }
+    });
+  }
+  // Initialize when DOM is ready
+  if (document.readyState === 'loading') {
+    document.addEventListener('DOMContentLoaded', initHamburgerMenu);
+  } else {
+    initHamburgerMenu();
+  }
+})();
+</script>
+<script>
+  (function() {
+    // Clone the page TOC for floating TOC
+    function initFloatingTOC() {
+      var pageTOC = document.getElementById('page-toc-top');
+      var floatingTOCContent = document.getElementById('floating-toc-content');
+      var floatingTOC = document.getElementById('floating-toc');
+      if (!pageTOC || !floatingTOCContent || !floatingTOC) return;
+      // Clone the TOC structure
+      var tocClone = pageTOC.cloneNode(true);
+      tocClone.id = 'floating-toc-clone';
+      floatingTOCContent.appendChild(tocClone);
+      // Update all links to use smooth scrolling
+      var allTOCLinks = document.querySelectorAll('.page-toc a, .floating-toc-content a');
+      allTOCLinks.forEach(function(link) {
+        link.addEventListener('click', function(e) {
+          var href = this.getAttribute('href');
+          if (href && href.startsWith('#')) {
+            e.preventDefault();
+            var targetId = href.substring(1);
+            var targetElement = document.getElementById(targetId);
+            if (targetElement) {
+              var offset = 20; // Offset from top
+              // Function to calculate absolute position from document top
+              function getAbsoluteTop(element) {
+                var top = 0;
+                while (element) {
+                  top += element.offsetTop;
+                  element = element.offsetParent;
+                }
+                return top;
+              }
+              var absoluteTop = getAbsoluteTop(targetElement);
+              var scrollTop = window.pageYOffset || document.documentElement.scrollTop;
+              var offsetPosition = absoluteTop - offset;
+              // Only scroll if we're not already at the target position
+              if (Math.abs(scrollTop - offsetPosition) > 10) {
+                window.scrollTo({
+                  top: Math.max(0, offsetPosition),
+                  behavior: 'smooth'
+                });
+              }
+              // Update URL hash without triggering scroll
+              if (history.pushState) {
+                history.pushState(null, null, href);
+              }
+            }
+          }
+        });
+      });
+      // Handle scroll to show/hide floating TOC
+      var tocTop = pageTOC.getBoundingClientRect().top + window.pageYOffset;
+      var tocBottom = tocTop + pageTOC.offsetHeight;
+      function updateFloatingTOC() {
+        var scrollY = window.pageYOffset || document.documentElement.scrollTop;
+        if (scrollY > tocBottom) {
+          floatingTOC.classList.add('visible');
+        } else {
+          floatingTOC.classList.remove('visible');
+        }
+      }
+      // Throttle scroll events
+      var ticking = false;
+      window.addEventListener('scroll', function() {
+        if (!ticking) {
+          window.requestAnimationFrame(function() {
+            updateFloatingTOC();
+            ticking = false;
+          });
+          ticking = true;
+        }
+      });
+      // Initial check
+      updateFloatingTOC();
+    }
+    // Initialize when DOM is ready
+    if (document.readyState === 'loading') {
+      document.addEventListener('DOMContentLoaded', initFloatingTOC);
+    } else {
+      initFloatingTOC();
+    }
+  })();
+</script>
+<footer class="page-footer"><p>Copyright 2025 Brett Terpstra, All Rights Reserved | MIT License</p></footer></body>
+</html>